Thanks to Rhimrifer for pointing it out, seems there were some spots where bots may have been getting stuck, this *should* be fixed now.
No idea who is to blame for this bug, me or Valve. MVM is designed to go to the next logical mission in their mission cycles. I.E. An advanced mission to the next map's advanced mission. But for some reason, MVM reloads maps during the loading process and this never happens.
By forcing the server to switch to the next logical map/mission manually after the end of game countdown, this issue doesn't happen!